<tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
    <description>uses the output from computeGCBias to generate GC-corrected BAM files</description>
    <macros>
        <token name="@BINARY@">correctGCBias</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        ln -s "$bamInput" "local_bamInput.bam" &&
        ln -s "$bamInput.metadata.bam_index" local_bamInput.bam.bai &&

        @BINARY@
            @THREADS@
            --bamfile local_bamInput.bam
            --GCbiasFrequenciesFile "$GCbiasFrequenciesFile"

            @reference_genome_source@

            #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
            #else:
                --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
            #end if

            #if str($region).strip() != '':
                --region '$region'
            #end if
            --correctedFile corrected.bam
]]>
    </command>
    <inputs>
        <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" />
        <param argument="--bamInput" format="bam" type="data"
            label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted." />
        <expand macro="reference_genome_source" />
        <expand macro="effectiveGenomeSize" />
        <expand macro="region_limit_operation" />
    </inputs>
    <outputs>
        <data format="bam" from_work_dir="corrected.bam" name="outFileName" />
    </outputs>
    <tests>
        <test>
            <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
            <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
            <param name="ref_source" value="history" />
            <param name="input1" value="sequence.2bit" />
            <param name="effectiveGenomeSize_opt" value="specific" />
            <param name="effectiveGenomeSize" value="23011544" />
            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed in
Benjamini and Speed (2012) Nucleic Acids Res.
The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.

You can find more details on the correctGCBias doc page: https://deeptools.readthedocs.org/en/master/content/tools/correctGCBias.html


**Output files**:

- GC-normalized BAM file

-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>